Origin IGS: tataaataactttttcccctgtacttcatcttgagaaaacaagttaccgtaatgcacaggagacttaagcagctccttcactttttcatatttttcaacccattctttttccggtatcatcgtatagacctccatgtagtcattgaatagtataatatttatcagtacatgtgtccacagacaaaagtctcattttttgatatacttataaaaagcttttataaggggttaaact .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 agtttaaccccttataaaagctttttataagtatatcaaaaaatgagacttttgtctgtggacacatgtactgataaatattatactattcaatgactacatggaggtctatacgatgataccggaaaaagaatgggttgaaaaatatgaaaaagtgaaggagctgcttaagtctcctgtgcattacggtaacttgttttctcaagatgaagtacaggggaaaaagttatttata Mask Tandem Repeat Region ================================================ tataaataactttttcccctgtacttcatcttgagaaaacaagttaccgtaatgcacaggagacttaagcagctccttcactttttcatatttttcaacccattctttttccggtatcatcgtatagacctccatgtagtcattgaatagtataatatttatcagtacatgtgtccacagacaaaagtctcattttttgatatacttataaaaagcttttataaggggttaaact Find is-nt database================================================ Query_seq: TDE0523:TDE0524|TDE0523:TDE0524:hypothetical protein:hypothetical protein:<-->:569922..570156 235 tataaataactttttcccctgtacttcatcttgagaaaacaagttaccgtaatgcacaggagacttaagcagctccttcactttttcatatttttcaacccattctttttccggtatcatcgtatagacctccatgtagtcattgaatagtataatatttatcagtacatgtgtccacagacaaaagtctcattttttgatatacttataaaaagcttttataaggggttaaact Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TDE0523:TDE0524|TDE0523:TDE0524:hypothetical protein:hypothetical protein:<-->:569922..570156 235 tataaataactttttcccctgtacttcatcttgagaaaacaagttaccgtaatgcacaggagacttaagcagctccttcactttttcatatttttcaacccattctttttccggtatcatcgtatagacctccatgtagtcattgaatagtataatatttatcagtacatgtgtccacagacaaaagtctcattttttgatatacttataaaaagcttttataaggggttaaact Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TDE0523:TDE0524|TDE0523:TDE0524:hypothetical protein:hypothetical protein:<-->:569922..570156 235 tataaataactttttcccctgtacttcatcttgagaaaacaagttaccgtaatgcacaggagacttaagcagctccttcactttttcatatttttcaacccattctttttccggtatcatcgtatagacctccatgtagtcattgaatagtataatatttatcagtacatgtgtccacagacaaaagtctcattttttgatatacttataaaaagcttttataaggggttaaact Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 tataaataactttttcccctgtacttcatcttgagaaaacaagttaccgtaatgcacaggagacttaagcagctccttcactttttcatatttttcaacccattctttttccggtatcatcgtatagacctccatgtagtcattgaatagtataatatttatcagtacatgtgtccacagacaaaagtctcattttttgatatacttataaaaagcttttataaggggttaaact Predict ORF larger than 30AA ================================================ Protein_Len: 43 Strand: + Start: 19 End: 147 .................. M Y F I L R K Q V T V M H R R L K Q L L H F F I F F N P F F F R Y H R I D L H V V I E ........................................................................................ Protein_Len: 60 Strand: - Start: 1 End: 180 I F L K K G Q V E D Q S F L N G Y H V P S K L L E K V K E Y K E V W E K E P I M T Y V E M Y D N F L I I N I L V H T W M ....................................................... tataaataactttttcccctgtacttcatcttgagaaaacaagttaccgtaatgcacaggagacttaagcagctccttcactttttcatatttttcaacccattctttttccggtatcatcgtatagacctccatgtagtcattgaatagtataatatttatcagtacatgtgtccacagacaaaagtctcattttttgatatacttataaaaagcttttataaggggttaaact Predict Promoter with matrix: RpoD-15 score > 80================================================ Predict Promoter with matrix: RpoD-16 score > 80================================================ Predict Promoter with matrix: RpoD-17 score > 80================================================ PromScan Matrix: RpoD-17 Strand: + Score: 85 Start: 91 End: 120 ..........................................................................................TTTTTCAACCCATTCTTTTTCCGGTATCAT................................................................................................................... PromScan Matrix: RpoD-17 Strand: - Score: 83 Start: 149 End: 178 ....................................................................................................................................................GTGGACACATGTACTGATAAATATTATACT......................................................... PromScan Matrix: RpoD-17 Strand: + Score: 82 Start: 196 End: 225 ...................................................................................................................................................................................................TTTGATATACTTATAAAAAGCTTTTATAAG.......... Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ tataaataactttttcccctgtacttcatcttgagaaaacaagttaccgtaatgcacaggagacttaagcagctccttcactttttcatatttttcaacccattctttttccggtatcatcgtatagacctccatgtagtcattgaatagtataatatttatcagtacatgtgtccacagacaaaagtctcattttttgatatacttataaaaagcttttataaggggttaaact Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: TDE0523:TDE0524|TDE0523:TDE0524:hypothetical protein:hypothetical protein:<-->:569922..570156 235 tataaataactttttcccctgtacttcatcttgagaaaacaagttaccgtaatgcacaggagacttaagcagctccttcactttttcatatttttcaacccattctttttccggtatcatcgtatagacctccatgtagtcattgaatagtataatatttatcagtacatgtgtccacagacaaaagtctcattttttgatatacttataaaaagcttttataaggggttaaact Intra-Species Hit: Count: 1 Min: 1 Max: 235 Len: 235 Subject: NC_002967_TDE0523_TDE0524|hypothetical protein:hypothetical protein|NEGATIVE:POSITIVE|[569922,570156]|235 HSP 1 e-value: 1.0E-130 bit: 466.0 Len: 235 Query Start:1 Query End:235 Subject Strand: POSITIVE Subject Start: 1 Subject End: 235 tataaataactttttcccctgtacttcatcttgagaaaacaagttaccgtaatgcacaggagacttaagcagctccttcactttttcatatttttcaacccattctttttccggtatcatcgtatagacctccatgtagtcattgaatagtataatatttatcagtacatgtgtccacagacaaaagtctcattttttgatatacttataaaaagcttttataaggggttaaact tataaataactttttcccctgtacttcatcttgagaaaacaagttaccgtaatgcacaggagacttaagcagctccttcactttttcatatttttcaacccattctttttccggtatcatcgtatagacctccatgtagtcattgaatagtataatatttatcagtacatgtgtccacagacaaaagtctcattttttgatatacttataaaaagcttttataaggggttaaact Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ UAUAAAUAACUUUUUCCCCUGUACUUCAUCUUGAGAAAACAAGUUACCGUAAUGCACAGGAGACUUAAGCAGCUCCUUCACUUUUUCAUAUUUUUCAACCCAUUCUUUUUCCGGUAUCAUCGUAUAGACCUCCAUGUAGUCAUUGAAUAGUAUAAUAUUUAUCAGUACAUGUGUCCACAGACAAAAGUCUCAUUUUUUGAUAUACUUAUAAAAAGCUUUUAUAAGGGGUUAAACU ..........(((..(((((..........((((((((....((.........))..(((((.((.....))))))).............))))))))......((((((..(((((.((((.((((((...((((((.(...((((((......))))))..).))))))((((....))))...)))).))....)))))))))...))))))........)))))..))).. (-39.70) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AGUUUAACCCCUUAUAAAAGCUUUUUAUAAGUAUAUCAAAAAAUGAGACUUUUGUCUGUGGACACAUGUACUGAUAAAUAUUAUACUAUUCAAUGACUACAUGGAGGUCUAUACGAUGAUACCGGAAAAAGAAUGGGUUGAAAAAUAUGAAAAAGUGAAGGAGCUGCUUAAGUCUCCUGUGCAUUACGGUAACUUGUUUUCUCAAGAUGAAGUACAGGGGAAAAAGUUAUUUAUA ..((((((((((((((((.....))))))))..(((((.......((((....))))((((((.((((((.(.((.((((......))))..)).).))))))...))))))....))))).............))))))))............(((((..((((.......((((((((((.((.((....((((......)))).))))))))))))))...)))).))))). (-52.20) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 901 80 31 171 122 NC_002967:TDE0523|5end_hypothetical_protein_569831..570061_NEGATIVE 340 140 98 106 65 NC_002967:TDE1261|5end_choline/carnitine/betaine_transporter_family_protein_1295593..1295823_POSITIVE 303 134 94 76 31 NC_002967:TDE0248|5end_hypothetical_protein_282068..282298_POSITIVE 302 134 92 109 60 NC_002967:TDE2632|5end_peptide_ABC_transporter,_ATP-binding_protein,_putative_2672650..2672880_POSITIVE 293 133 95 102 60 NC_002967:TDE1084|5end_folylpolyglutamate_synthetase,_putative_1116286..1116516_NEGATIVE 292 70 24 49 2 NC_002967:TDE1849|5end_hypothetical_protein_1878123..1878353_NEGATIVE 276 60 11 173 95 NC_002967:TDE0654|5end_peptidase,_M20/M25/M40_family_689606..689836_POSITIVE 271 140 91 137 78 NC_002967:TDE2425|5end_50S_ribosomal_protein_L11_2455150..2455380_NEGATIVE 271 87 47 59 22 NC_002967:TDE1027|5end_ribonuclease_III_1057562..1057792_POSITIVE 269 119 71 222 175 NC_002967:TDE1216|5end_flagellar_motor_protein_1248441..1248671_POSITIVE 264 147 104 71 27 NC_002967:TDE1900|5end_hypothetical_protein_1921124..1921354_POSITIVE 262 88 47 86 43 NC_002967:TDE0304|5end_hypothetical_protein_333883..334113_POSITIVE 258 160 112 129 71 NC_002967:TDE1504|5end_ribosomal_protein_L31_1553350..1553580_POSITIVE 257 140 109 37 13 NC_002967:TDE1072|5end_lipoprotein,_putative_1100741..1100971_POSITIVE 256 137 91 207 163 NC_002967:TDE0314|5end_hypothetical_protein_346077..346307_POSITIVE 255 136 111 31 4 NC_002967:TDE1499|5end_adenylosuccinate_lyase,_putative_1545266..1545496_POSITIVE 254 87 58 218 185 NC_002967:TDE0122|5end_dihydrouridine_synthase,_putative_141539..141769_NEGATIVE 252 140 103 56 17 NC_002967:TDE0455|5end_kinase,_GHMP_family_511192..511422_POSITIVE 251 77 41 65 32 NC_002967:TDE2643|5end_oxidoreductase,_FAD-dependent_2682185..2682415_POSITIVE 251 60 18 98 58 NC_002967:TDE1824|5end_hypothetical_protein_1857011..1857241_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 340 140 98 109 68 NC_002967:TDE1260|3end_cholinephosphate_cytidylyltransferase/choline_kinase_1295676..1295826_POSITIVE 302 134 92 112 63 NC_002967:TDE2631|3end_peptide_ABC_transporter,_permease_protein,_putative_2672733..2672883_POSITIVE 258 160 112 92 34 NC_002967:TDE1503|3end_transcription_termination_factor_Rho_1553393..1553543_POSITIVE 252 140 91 145 102 NC_002967:TDE2103|3end_glycosyl_transferase,_group_2_family_protein_2127527..2127677_NEGATIVE 251 138 92 66 16 NC_002967:TDE0221|3end_hypothetical_protein_254046..254196_NEGATIVE 248 135 93 108 70 NC_002967:TDE0369|3end_type_I_restriction-modification_system,_M_subunit_418356..418506_NEGATIVE 247 70 24 85 43 NC_002967:TDE0098|3end_hypothetical_protein_114842..114992_NEGATIVE 246 80 40 49 4 NC_002967:TDE2117|3end_hypothetical_protein_2149175..2149325_POSITIVE 245 123 81 151 102 NC_002967:TDE0888|3end_hypothetical_protein_904733..904883_NEGATIVE 244 144 101 105 53 NC_002967:TDE2563|3end_hypothetical_protein_2590068..2590218_POSITIVE 240 79 36 69 32 NC_002967:TDE2558|3end_ABC_transporter,_ATP-binding/permease_protein_2583729..2583879_NEGATIVE 240 89 44 55 3 NC_002967:TDE2156|3end_translation_initiation_factor_IF-3_2190192..2190342_NEGATIVE 235 87 53 35 3 NC_002967:TDE1026|3end_acyl_carrier_protein_1057618..1057768_POSITIVE 235 87 41 122 50 NC_002967:TDE0461|3end_hypothetical_protein_516125..516275_POSITIVE 234 137 91 134 87 NC_002967:TDE1526|3end_hypothetical_protein_1570887..1571037_POSITIVE 233 112 76 118 82 NC_002967:TDE1206|3end_TPR_domain_protein_1239312..1239462_POSITIVE 231 86 53 144 109 NC_002967:TDE2047|3end_hypothetical_protein_2076058..2076208_NEGATIVE 231 169 121 47 7 NC_002967:TDE0251|3end_tryptophanase_284717..284867_NEGATIVE 231 133 97 74 33 NC_002967:TDE0075|3end_sorbitol_dehydrogenase,_putative_85527..85677_NEGATIVE 230 81 41 127 86 NC_002967:TDE2623|3end_hypothetical_protein_2663584..2663734_NEGATIVE